Electric double-layer capacitors (EDLCs) are advanced electrochemical devices that have attracted tremendous attention because of their high power density, ultra-fast charging/discharging rate, and superior lifespan. A major challenge is how to further improve their energy density. At present, a large number of research efforts are primarily focusing on engineering the morphology and microstructure of electrodes to achieve better performance, for example, enlarging the specific surface area and designing the pore size. More importantly, wettability plays a crucial role in maximizing the effective utilization and accessibility of electrode materials. However, its primary mechanisms/phenomena are still partially resolved. Here, we explore the effects of wettability on the charging dynamics of EDLCs using molecular dynamics (MD) simulations. Typically, hydrophobic graphene (GP) and hydrophilic copper (Cu) are employed as the electrode materials. Differential capacitances (CD) as a function of electrode potentials (ϕ) are computed by means of Poisson and Gaussian equation calculations. Simulation results show that during the charging process of EDLCs, the differential capacitances of hydrophobic GP are insensitive to the electrode potentials. However, superhydrophilic Cu electrode exhibits an asymmetric U-shaped CD–ϕ curve, in which the capacitance at the negative polarization can be ~5.77 times greater than that of the positive counterpart. Such an unusual behavior is obviously different with the conventional Gouy-Chapman-Stern theory (i.e., symmetric U-shaped), room temperature ionic liquids (i.e., camel-, or bell-shaped), and hydrophobic counterpart, which is closely correlated with the free energy barrier distributions. Compared with the positive polarization or hydrophobic case, the energy barriers near the negative hydrophilic electrodes are remarkably suppressed, which benefits ion populations at the interface and enables the convenient orientation or distribution of ions to shield the external electric fields from electrodes, thereby yielding higher differential capacitances. With differentiating the ion charge density, the as-obtained CD–ϕ curves are well resembled, quantitatively establishing the correlations between EDL microstructures and differential capacitances. Besides, we also point out that enhancing the wettability could significantly decrease the EDL thickness from ~1.0 nm (hydrophobic) to ~0.5 nm (hydrophilic). In the end, we demonstrate that wetting property also impacts a prominent role in the charge storage behavior of EDLCs, transforming the charging mechanism dominated by counter-ion adsorption and ion exchange (hydrophobic) to pure counter-ion adsorption (hydrophilic). The as-obtained insights highlight the significance of wettability in regulating charging dynamics and mechanisms, providing useful guidelines for precisely controlling the wetting property of electrode materials for advanced charge storage of EDLCs.